Genome-wide identification and characterization of the antifreeze protein gene family in rainbow trout (Oncorhynchus mykiss): An in silico perspective

Abstract:

Antifreeze proteins (AFPs) represent a remarkable adaptation enabling organisms to survive in sub-zero environments by inhibiting ice crystal formation and growth. Despite their critical role in cold tolerance and significant implications for aquaculture productivity in temperate regions, comprehensive genome-wide analyses of AFP gene families in economically important salmonids remain limited. This study presents the first systematic genome-wide identification and comprehensive characterization of the antifreeze protein gene family in rainbow trout (Oncorhynchus mykiss), one of the most economically valuable cold-water aquaculture species globally. Our analysis identified one complete antifreeze protein gene (antifreeze protein Maxi-like BETA, Gene ID: 118943589) in the rainbow trout genome using the USDA_OmykA_1.1 assembly. The gene exhibits a compact genomic structure with a length of 624 bp, encoding a complete coding sequence (CDS) of 624 bp (207 amino acids) organized into 4 exons and localized on chromosome 22 (NC_048586.1: 40380233-40386211). Physicochemical analysis revealed a small protein of 18.5 kDa with a basic isoelectric point (pI 9.10), extinction coefficient of 7115, and one predicted N-glycosylation site. Structural predictions identified conserved functional domains characteristic of Type II antifreeze proteins, with motif analysis revealing highly preserved sequences essential for ice-binding activity. Subcellular localization predictions indicated extracellular secretion, consistent with the protein’s role in preventing extracellular ice formation. Phylogenetic analysis demonstrated evolutionary conservation across teleost lineages, with the rainbow trout AFP clustering with other salmonid species, reflecting lineage-specific adaptations to cold environments. Beyond advancing fundamental understanding of molecular mechanisms underlying freeze tolerance in teleosts, this comprehensive genomic characterization provides essential resources for applied aquaculture applications, including identification of molecular markers for selective breeding programs targeting enhanced cold tolerance, development of cryoprotective strategies, and optimization of production in cold-water aquaculture systems. Our results establish a foundational genomic resource for future functional studies of AFP genes in salmonids, bridging evolutionary biology with practical aquaculture biotechnology.